Continuum Removal

Recently, I was given the chance to practice some
spectroscopy and in preparation for the project, I realized that I did not have
a simple way to visualize the variations in different absorption features
between very discreet wavelengths. The method that I elected to employ for this
task is called continuum removal
(Kokaly, Despain, Clark, & Livo, 2007). This method allows you to
compare different spectra and essentially normalize the data so that they can
be more easily compared with one another.

To use the algorithm, you first select the region that you
are interested in (for me this was between 550 nm and 700 nm -this is the
region of my spectra that deals with chlorophyll absorption and pigment). Once
the region is selected then a linear model is fit between the two points and
this is called the continuum. The continuum is the hypothetical background
absorption feature, or artifact or other absorption feature, which acts as the
baseline for the target features to be compared against (Clark, 1999). Once the
continuum has been set then the continuum removal process can be performed on
all spectra in questionusing
the following equation (Kokaly,
Despain, Clark, & Livo, 2007).

RC is
the resulting continuum removed spectra, RL is the continuum line
and, Ro is the original reflectance value.

Figure 1:
Original spectra of two healthy plants. The dotted line denotes the continuum
line. The x axis shows wavelengths in nm and the y axis represents reflectance.

Figure 2: The
continuum removal for wavelengths 550 nm - 700 nm.

The resulting code gives you a tool that will take in two
spectral libraries, with one spectra per library, and return two plots similar
to what is shown in Figure 1 and Figure 2.